List of works by Ivo L. Hofacker

2D meets 4G: G-quadruplexes in RNA secondary structure prediction

scientific article published in July 2013

A folding algorithm for extended RNA secondary structures ⬇️

scientific article published on July 2011

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

scientific article published on 23 November 2015

AREsite: a database for the comprehensive investigation of AU-rich elements

scientific article

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation

scientific article

Algorithm independent properties of RNA secondary structure predictions

article published in 1996

Alignment of RNA base pairing probability matrices

scientific article

Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.

scientific article

Animal snoRNAs and scaRNAs with exceptional structures

scientific article published on November 2011

Arthropod 7SK RNA.

scientific article

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

scientific article published on 4 September 2013

BarMap: RNA folding on dynamic energy landscapes

scientific article

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes

scientific article published on 19 March 2014

Bcheck: a wrapper tool for detecting RNase P RNA genes

scientific article

Beyond energy minimization: approaches to the kinetic folding of RNA

CMCompare webserver: comparing RNA families via covariance models

scientific article (publication date: July 2013)

CMV: visualization for RNA and protein family models and their comparisons

scientific article published on 01 August 2018

Challenges in RNA virus bioinformatics

scientific article published on 03 March 2014

Comparative RNA Genomics

scientific article published in January 2018

Comparative genomics of Czech vaccine strains of Bordetella pertussis

scholarly article by Ana Dienstbier et al published 3 September 2018 in Pathogens and disease

Complete suboptimal folding of RNA and the stability of secondary structures.

scientific article published in February 1999

Computational Design of a Circular RNA with Prionlike Behavior.

scientific article published on 2 March 2016

Computational design of RNAs with complex energy landscapes

scientific article

Concepts and introduction to RNA bioinformatics

scientific article published on January 2014

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

scientific article

Conserved RNA secondary structures in Flaviviridae genomes

scientific article

Conserved RNA secondary structures in viral genomes: a survey.

scientific article published in July 2004

Conserved Secondary Structures in Viral mRNAs.

scientific article published on 29 April 2019

Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs

article

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

scientific article

De novo prediction of structured RNAs from genomic sequences

scientific article

Design of multistable RNA molecules

scientific article

Designing optimal siRNA based on target site accessibility.

scientific article published in January 2010

Detection of RNA structures in porcine EST data and related mammals.

scientific article

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

scientific article

Discriminatory power of RNA family models ⬇️

scientific article (publication date: 15 September 2010)

Efficient computation of RNA folding dynamics

article

Efficient computation of co-transcriptional RNA-ligand interaction dynamics

Efficient computation of co-transcriptional RNA-ligand interaction dynamics

scholarly article by Michael T. Wolfinger published in July 2018

Energy-directed RNA structure prediction

scientific article published on January 2014

Enhancing the cell-free expression of native membrane proteins by in-silico optimization of the coding sequence – an experimental study of the human voltage-dependent anion channel

Evolution of metabolic networks: a computational frame-work

article

Evolutionary Genomics of microRNAs and Their Relatives

article published in 2010

Evolutionary patterns of non-coding RNAs

scientific article published on 01 April 2005

Exploring the lower part of discrete polymer model energy landscapes

article

Fast accessibility-based prediction of RNA-RNA interactions

scientific article published on 18 May 2011

Fast and reliable prediction of noncoding RNAs

scientific article

Folding RNA/DNA hybrid duplexes

scientific article published on 24 July 2012

Folding kinetics of large RNAs

scientific article published on 6 March 2008

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

scientific article published on 22 June 2015

From consensus structure prediction to RNA gene finding

scientific article

From structure prediction to genomic screens for novel non-coding RNAs

scientific article

Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

scientific article published on 24 March 2019

How microRNAs choose their targets

How to Multiply Dynamic Programming Algorithms

Hybridization thermodynamics of NimbleGen microarrays.

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

scientific article published on 9 May 2013

Impact of Hfq on the Bacillus subtilis transcriptome

scientific article

In silico design of ligand triggered RNA switches

In silico design of ligand triggered RNA switches.

scientific article published on 13 April 2018

Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

scientific article

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

scientific article published on 31 December 2021

Interactions in Oligonucleotide Hybrid Duplexes on Microarrays

article published in 2004

Invertebrate 7SK snRNAs.

scientific article published on 12 January 2008

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

scientific article published on 26 March 2012

Local RNA base pairing probabilities in large sequences.

scientific article published on 20 December 2005

MSF: Modulated Sub-graph Finder

scientific article published on 29 August 2018

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

article published in 2005

Memory efficient folding algorithms for circular RNA secondary structures

scientific article

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

scientific article

Model-based probe set optimization for high-performance microarrays

scientific article

Modelling translation initiation under the influence of sRNA

scientific article published on 30 November 2012

Multiple sequence alignments of partially coding nucleic acid sequences

scientific article

NMR structural profiling of transcriptional intermediates reveals riboswitch regulation by metastable RNA conformations

scientific article

Nematode sbRNAs: homologs of vertebrate Y RNAs

scientific article

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

scientific article

Nucleic acid sequence and structure databases

scientific article published on January 2010

On the evolution of primitive genetic codes

article

Optimizing RNA structures by sequence extensions using RNAcop

scientific article

Oxygen and proton pathways in cytochrome c oxidase

scientific article published on 01 January 1998

Partition function and base pairing probabilities of RNA heterodimers

scientific article

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks

scientific article

Predicting RNA 3D structure using a coarse-grain helix-centered model

scientific article

Predicting RNA secondary structures from sequence and probing data

scientific article

Predicting RNA structure: advances and limitations

scientific article published in January 2014

Prediction of RNA base pairing probabilities on massively parallel computers.

scientific article published in February 2000

Prediction of consensus RNA secondary structures including pseudoknots.

scientific article published in April 2004

Prediction of locally stable RNA secondary structures for genome-wide surveys

scientific article published in January 2004

Primary relaxation in a hard-sphere system

scientific article published on 01 January 1992

Product Grammars for Alignment and Folding

scientific article published on May 2015

Pseudoknots in RNA folding landscapes.

scientific article

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets

scientific article published on 20 January 2017

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

scientific article published on 28 October 2015

RNA Accessibility in cubic time

scientific article published on 9 March 2011

RNA Consensus Structure Prediction With RNAalifold

RNA Folding Algorithms with G-Quadruplexes

RNA In Silico The Computational Biology of RNA Secondary Structures

RNA Secondary Structures

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates

article

RNA folding and combinatory landscapes

scientific article published on 01 March 1993

RNA folding at elementary step resolution

scientific article

RNA folding with hard and soft constraints

scientific article (publication date: 2016)

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

scientific article

RNA modifications in structure prediction - status quo and future challenges

scientific article published on 30 October 2018

RNA secondary structure analysis using the Vienna RNA package.

scientific article published in June 2009

RNAalifold: improved consensus structure prediction for RNA alignments

scientific article

RNAblueprint: Flexible multiple target nucleic acid sequence design

scientific article published on 25 April 2017

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

scientific article

RNAlien - Unsupervised RNA family model construction

scientific article

RNAplex: a fast tool for RNA-RNA interaction search

scientific article published on 23 April 2008

RNApredator: fast accessibility-based prediction of sRNA targets

scientific article

RNAs everywhere: genome-wide annotation of structured RNAs

scientific article

RNAsnoop: efficient target prediction for H/ACA snoRNAs

scientific article published on 16 December 2009

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced bySNPs.

scientific article published on 15 March 2013

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs

scientific article

RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles

scientific article

SHAPE directed RNA folding

scientific article published on 9 September 2015

SHAPE directed RNA folding

Secondary structure prediction for aligned RNA sequences

scientific article (publication date: 21 June 2002)

Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.

scientific article

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

scientific article

SnoReport: computational identification of snoRNAs with unknown targets

scientific article

Strategies for measuring evolutionary conservation of RNA secondary structures

scientific article

Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon

scientific article

Structural parameters affecting the kinetics of RNA hairpin formation

scientific article published on 19 July 2006

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

Symmetric circular matchings and RNA folding

TSSAR: TSS annotation regime for dRNA-seq data

scientific article

The RNAsnp web server: predicting SNP effects on local RNA secondary structure

scientific article published on 29 April 2013

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

scientific article

The Trouble with Long-Range Base Pairs in RNA Folding

article published in 2013

The Vienna RNA websuite

scientific article

The expansion of the metazoan microRNA repertoire

scientific article

The impact of target site accessibility on the design of effective siRNAs

scientific article published on 27 April 2008

Thermodynamic and kinetic folding of riboswitches

scientific article

Thermodynamics of RNA-RNA binding

scientific article

Transcriptional profiling of human macrophages during infection with Bordetella pertussis

scientific article published on 19 February 2020

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

scientific article published on 25 October 2016

Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution

scientific article published on 13 May 2016

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate

scientific article

Variations on RNA folding and alignment: lessons from Benasque.

scientific article

Vienna RNA secondary structure server

scientific article (publication date: July 2003)

ViennaRNA Package 2.0

scientific article

Visualization of Barrier Tree Sequences Revisited

scholarly article by Christian Heine et al published 2008 in Mathematics and visualization

Visualization of barrier tree sequences.

scientific article published in September 2006

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

scientific article published on 09 January 2020

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.

scientific article published on 27 September 2016

www.rnaworkbench.com: A new program for analyzing RNA interference.

scientific article published on 22 January 2008

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